Have you tried binary xoring the strings? Zeros will occur in positions that are occupied by the same letter, the other results are unique for all combinations. 
perl -e '$s1 = "AAAACCCCTTTTGGGG";
    $s2 = "ACTGACTGACTGACTG";
    print $s1 ^ $s2; ' | hexdump
00000000  00 02 15 06 02 00 17 04  15 17 00 13 06 04 13 00

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In reply to Re: mismatching characters in dna sequence by choroba
in thread mismatching characters in dna sequence by prbndr

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